towards a practical knowledgebase for marine genetic resources · chelicerata uniramia chaetognatha...
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Towards a practical knowledgebase for marine genetic resources
Libby Evans-Illidge
Manager Bioresources Library, Australian Institute of Marine Science, PMB 3 Townsville MC, 4810, Queensland, Australia.
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Marine Benthic
Marine Pelagic
Freshwater Benthic
Freshwater Pelagic
Terrestrial Moist
Terrestrial xeric
Symbiotic ecto
Symbiotic endo
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Phyla/Sub-Phyla
HabitatNumber*
*1=1-100
2=100-1,000
3=1,000-10,000
4=10,000-100,000
5=>100,000
The seafloor is the most biodiverse place on earth- Based on diversity of macro-organisms
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Superimposed with bacterial symbiont diversity
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R 177
R 185
R 7
R 141
R 43
R006R 98R 165R 78
R 214R 219
R 171R 11 R 18
R 124
R 84
R 19R 106
R 122R 130
E.coliR 180
R 58
R 187
R 93
R 13R 202
R 14R 211
R 28
R 140R 63
R 33 R 25
R 125
Subgroup II
Subgroup III
Subgroup I(Predominantly Actinobacteria)
(Predominantly Green Non-Sulfur and δ- Proteobacteria)
(Predominantly γ- Proteobacteria)
30%
41%
29%
eg. Microorganisms found in the stable community within the Great Barrier Reef sponge Rhopaloeides odorabile. (Nicole Webster)
Marine Natural Products and Related Compounds in Clinical and AdvancedPreclinical TrialsTable 1. Status of Marine-Derived Natural Products in Clinical and Preclinical Trialsname source status (disease) comment
didemnin B Trididemnum solidum Phase II (cancer) dropped middle 90sdolastatin 10 Dolabella auricularia(marine microbe derived;cyanophyte) Phase I/II (cancer) no further trialsgirolline Pseudaxinyssa cantharella Phase I (cancer) discontinuedbengamide Jaspis sp. Phase I (cancer) licensed Novartiscryptophycins Nostoc sp. & Dysidea arenaria Phase I (cancer) licensed to Lilly bryostatin 1 Bugula neritina Phase II (cancer) licensed to GPC Biodolastatin Dollabella Phase II (cancer) melanoma, breast,ecteinascidin Ecteinascidia turbinata Phase II/III (cancer) licensed to J&Japlidine Aplidium albicans Phase II (cancer) E7389 (Hali B) Lissodendoryx sp Phase I (cancer) Eisaidiscodermolide Discodermia dissoluta Phase I (cancer) licensed to Novartiskahalalide F Eylsia rufescens/Bryopsis sp. Phase II (cancer) licensed to PmMarSpisulosine Spisula polynyma Phase I (cancer) Rho-GTP inhibitorHTI-286 Cymbastella sp Phase II (cancer) licensed to WyethKRN-7000 Agelas mauritianus Phase I (cancer) squalamine Squalus acanthias Phase II (cancer) antiangiogenicLaulimalide Cacospongia mycofijiensis preclinical (cancer)Curacin A Lyngbya majuscula preclinical (cancer)vitilevuamide Didemnum cucliferum &Polysyncraton lithostrotum preclinical (cancer)diazonamide Diazona angulata preclinical (cancer) eleutherobin Eleutherobia sp. preclinical (cancer) sarcodictyin Sarcodictyon roseum preclinical (cancer)peloruside A Mycale hentscheli preclinical (cancer) Just licensedsalicylihalimide Haliclona sp. preclinical (cancer) thiocoraline Micromonospora marina preclinical (cancer) variolins Kirkpatrickia variolosa preclinical (cancer) dictyodendrins Dictyodendrilla verongiformis preclinical (cancer) licensed to Taihomanoalide Luffariaella variabilis Phase II discontinuedIPL-576,092 Petrosia contignata Phase II licensed to Aventisziconotide Conus magus Phase III pain licensed to WLCGX-1160 plus Conus geographus, catus, victoriae Phase I (pain)
Journal of Natural Products ReviewsDavid J. Newman* and Gordon M. CraggNatural Products Branch, Developmental Therapeutics Program, NCI-Frederick, P.O. Box B, Frederick, Maryland 21702Received February 10, 2004; see also Fortman and Sherman CC 2005@ 38% from Australasia
Cytarabine (Ara-A,C) from Cryptotheca crypta now routine for leukaemia and lymphoma patients, Glaxo Smith Kline and Pfizer
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Natural Products Natural Products ““RenaissanceRenaissance””(with a twist)(with a twist)
Paterson and Anderson, Science 21 October 2005
A significant cumulative effort in ocean exploration
‘Parents’ of marine science:•Indigenous observations over millennia•Aristotle 384-322BC•Charles Darwin HMS Beagle 1831-36•Challenger 1872-75
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Marine R&D technology in the 21st
Century
…but still so much remains unknown
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Where is the data? How can we access it?
• Specialist data• Published Literature • Portals for metadata• Networked datasets• Integrated datasets
Literature Databases•Cambridge Scientific Abstracts•Aquatic Sciences & Fisheries Abstracts•Zoological Record•Biosis•MarineLit•Patent databases
Citation & Indexing services
Citation data management
•Web of Science•Google Scholar
•Ref works•Endnote
The published literatureThe published literature
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Data Networks/RepositoriesData Networks/RepositoriesNucleotide sequencesNucleotide sequences
• INSDC (international Nucleotide Sequence Database Collaboration) www.insdc.org
– GenBank®, DDBJ, EMBL– Annotated collection of all publicly
available DNA sequences– Submission of sequences required by
many journals prior to publication– Online submission, update and review– Country of origin identified– No restriction on use or distribution– 73078143 loci, 77248690945
bases, from 73078143 reported sequences (June 15 2007)
• Data searching & analysis tools- eg. BLAST
www.ncbi.nlm.nih.gov/Genbank/
Specialist data – find the people
Location of specimen and data holdings reflects historical location of the specialists
eg. Scleractinian corals
•Major repository at Museum of Tropical Queensland, Townsville Australia
•Doorstep of Great Barrier Reef
•Home of 2 global experts -Dr Carden Wallace (MTQ) and Dr John Veron (AIMS, Townsville)
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UN Atlas of the Oceans
•UN-Oceans coordination portal•14 Global partners and 8000 individual members. •Peer reviewed. •Features a Virtual Office, advanced Search, web statistics and monthly newsletter. FREE TO MEMBERS•New marine genetics page
http://www.oceansatlas.org/
Castanospermum australeBelongs to the Fabaceae family, commonly referredto as Black Bean or the Moreton Bay Chestnut.
Beautiful large evergreen tree with glossy darkgreen pinnate leaves and low spreading brancheswhen grown in the open. During Spring it bearssprays of red and yellow pea-shaped flowers. Thelarge cylindrical pods which are produced in autumnand have 3-5 large bean like seeds inside. Thenectar produced by the flowers attracts birds, batsand butterflies.
Tree, to 35 m high with trunk up to 1.5 m diam,, but usuallysmaller, mostly glabrous. Leaves 30-60 cm long; leaflets 9-17,± oblong-elliptic, 7-20 cm long, 3-5 cm wide, apex acuminate,margins entire, glabrous, upper surface glossy, lower surfacepaler and dull; petiole 3-6 cm long; lateral petiolules 2-5 mmlong. Racemes mostly 5-15 cm long; pedicels 20-35 mm long.Calyx c. 10 mm long. Corolla 30-40 mm long, orange to red.Pod mostly 10-20 cm long, 4-6 cm diam., glabrous; seeds1-5, c. 30 mm diam., brown. Flowers spring.
EcologyGrows in well developed rain forest, but is oftenfound in gallery forest along creeks and rivers.
Source: Flora of NSW and Rain Forest Key
DistributionOccurs in Cape York Peninsula (CYP)and North East Queensland (NEQ),and southwards to north easternNew South Wales. Altitudinal rangein CYP and NEW from near sea levelto 800m. Also occurs in NewCaledonia and Vanutatu.
Name- APNI- Derivation
Description
Classification- Barcode of Life- Cladogram- Close relatives
Illustrations- Photographs- Line Drawings
Identification tools- Australian Tropical
Rain Forest Plants
Usage
Horticulture
Ethnobotany
Pharmacology
Current Research
Bibliography
National data network exampleNational data network example
•Searchable database, common format•all known Australian plant & animal species by 2015 •terrestrial and marine
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• It’s expensive ($40M, over 5 years)• Consistency in taxonomy is an issue
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• Growing global network• Assess and explain the diversity, distribution and
abundance of marine life in the world’s oceans• past, present and future• 2000 to 2010• 50+ countries, 300+ scientists, 17 major projects• Link to the Barcode of Life initiative
CoML defines its realms & zones in 2003 Baseline Report, The Unknown Ocean
Oceans Present: Realm ProjectsOceans Present: Realm Projects
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Ocean Realm Field Projects
Nearshore: NaGISAReefs: CReefsRegional Ecosystem: GoMAContinental Shelf: POST
Continental Margins: COMARGEAbyssal Plains: CeDAMar
Zooplankton: CMarZTop Predators: TOPPRidges: MAR-ECO
Vents & Seeps: ChEssSeamounts: CenSeam
Arctic: ArcODAntarctic: CAML
Microbes: ICOMM
Human Edges
Hidden BoundariesHidden Boundaries
Central WatersCentral Waters
Ice OceansIce Oceans
Microscopic OceanMicroscopic Ocean
Active GeologyActive Geology
Ocean Biogeographic Information System (OBIS) Portal www.iobis.org
OBIS strives to document the oceans' diversity,distribution, and abundance of life.
13.2 million records, 81000 species, 210 databasesSearchable on name or geographyConsistency in taxonomic assignment is an issue
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Assessment of Marine Genetic Resources- You need to know more than ‘where they occur’
Marine genetic resources are the integrated result of dynamic, complex ecology.
Battershill, unpublished
eg. •Activity of interest (HSV and PVI) in this example is only produced by sick sponges•Note high selectivity to the target (and absence of cytotoxicity)
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AIMS Bioresources Library – integrated MGR dataset
Fungi17%
Actinomycetes12%
Extremophyles12%
Bacteria59%
Cnidaria15%
Chordate13%
Plants10%
Echinodermata10%
Mollusca7%
Other5%
Bryozoa3%
Porifera37%
12000 macros
9000 micros
1987 – presentOver 1500 sites around Australia
COLLECTIONCOLLECTIONDATADATA
•Precise location•Depth•Size•Best taxonomy (voucher back-up)•Imagery•Coded descriptions
•habitat•morphology•substrate•colour(external/internal)•epibionts•symbionts
•Descriptive notes and observations •Site information (location, habitat description, community composition)
Micros:•Details of source and selective isolation
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A Bioresources Library for screening and A Bioresources Library for screening and biodiscovery (past, present, future)biodiscovery (past, present, future)
Cancer
Viral
Antibiotics
Central Nervous System
Agrichemical
Paints
Industrial Enzymes
Environmental remediation
Toxin detection
Mineral Processing
UV Blocking
Samples change format (and generate data) many times
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Bioinformatics – begins with sample info
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…integrated with other research outputs
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Integrated tool for data mining.eg. Regional and taxonomic patterns in anti-microbial activity
Analysis at a range of scales
Google Earth interface facilitates good visualisation of multi-variate data
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Understanding the chemical ecologyApply data-mining to enhance biodiscovery
• Elaborate leads – identifying other material with similar
taxonomy/ecology/ screening profile/chemistry– Naturally occurring analogues– Re-supply without re-collecting
• Predict results of future screening based on past profile– Compile list of pre-leads– Targeted biodiscovery with ex-situ material
Summary• Tools exist to access marine biodiversity and genetic
resources data that is in the global public domain• Major networking projects underway to bring together
independent geo-referenced datasets (CoML, ALA)• Consistency in taxonomy is a big issue in networking
independent datasets
• Integrated informatics is the ideal – Integrate biodiversity data (ecosystems, species (macro and
micro), genomes (and meta-genomes)), with natural products research outputs(instrument outputs, structures of compounds, proteins, enzymes etc), and screening results
– Powerful datamining tool to assess and understand marine genetic resources
– ‘Commercial in Confidence’ issues, but even a compilation of non-commercially sensitive information is useful
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Conservation of biodiversity is fundamental to the potential of marine genetic resources